3 Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
4 Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
6 This program is free software; you can redistribute it and/or
7 modify it under the terms of the GNU General Public License
8 as published by the Free Software Foundation; either version 2
9 of the License, or (at your option) any later version.
11 This program is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
16 You should have received a copy of the GNU General Public License
17 along with this program; if not, write to the Free Software
18 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
20 <project name="jalviewX" default="usage" basedir=".">
21 <!-- we use jalopy to format our sources -->
22 <taskdef name="jalopy"
23 classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
25 <fileset dir="utils/jalopy/lib">
26 <include name="*.jar" />
31 <target name="help" depends="usage"/>
33 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
34 <echo message="Targets include:"/>
35 <echo message="usage - default target, displays this message"/>
36 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
37 <echo message="build - compiles all necessary files for Application"/>
38 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
39 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
40 <echo message=" this needs a keystore and key. See docs/building.html for more information."/>
41 <echo message="compileApplet - compiles all necessary files for Applet"/>
42 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
43 <echo message="See docs/building.html and the comments in build file for other targets."/>
44 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
45 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
49 <!-- utils is a class path to additional utilities needed for
50 building docs, jars and webstart stuff -->
52 Userdefined build property defaults
54 wsdl.server list (plus namespace mapping info ???) - also want
55 ... to make this a dynamically generatable property
57 Build location - provide a temporary root for speed
58 jarsigner keystore and info
59 Jakarta and axis classpath ?
60 Default argument for starting Jalview (if it exists).
65 <path id="axis.classpath">
67 <fileset dir="/usr/local/axis/lib">
68 <include name="**/*.jar" />
70 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
71 <include name="**/*.jar"/>
72 <include name="*.jar"/>
75 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
76 <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
77 <!-- Include debugging information in javac true or false -->
78 <property name="javac.debug" value="true"/>
80 <!-- JarSigner Key Store for Webstart Distribution -->
81 <property name="jalview.keystore" value="./keys/.keystore"/>
82 <!-- Keystore Password -->
83 <property name="jalview.keystore.pass" value="alignmentisfun"/>
85 <property name="jalview.key" value="jalview"/>
87 <property name="jalview.key.pass" value="alignmentisfun"/>
89 <!-- Don't change anything below here unless you know what you are doing! -->
90 <!-- Url path for WebStart in JNLP file -->
91 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
92 <!-- build directory configuration -->
93 <property name="libDir" value="lib"/>
94 <property name="resourceDir" value="resources"/>
95 <property name="helpDir" value="help"/>
96 <property name="docDir" value="doc"/>
97 <property name="sourceDir" value="src" />
98 <property name="schemaDir" value="schemas" />
99 <property name="outputDir" value="classes" />
100 <property name="packageDir" value="dist" />
101 <property name="outputJar" value="jalview.jar" />
102 <!-- Jalview Applet JMol Jar Dependency -->
103 <property name="jmolJar" value="Jmol-11.0.2.jar" />
104 <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
105 <!-- switch to indicate if we should obfuscate jalviewLite -->
106 <!--<property name="donotobfuscate" value="true"/> -->
108 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
109 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
110 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
111 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
112 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
113 <property name="WSInterf" value="MsaWS" />
114 <property name="wsdl.Namespace" value="vamsas" />
115 <property name="wsdl.ClientNS" value="ext.vamsas" />
116 <!-- the class path for building the application -->
117 <path id="build.classpath">
118 <fileset dir="utils">
119 <include name="*.jar"/>
120 <include name="**/*.jar"/>
122 <fileset dir="${libDir}">
123 <include name="*.jar"/>
124 <include name="**/*.jar"/>
128 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
129 <!-- The Location of the java 1.1.8 jdk -->
130 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
131 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
132 <!-- jre for 1.4 version
133 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
135 <!-- the classpath for building the 1.1 applet -->
136 <path id="jalviewlite.deps">
137 <fileset dir="${java118.home}">
138 <include name="lib/classes.zip"/>
140 <pathelement location="lib/${jmolJar}"/>
145 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
146 <target name="buildPropertiesFile" depends="init">
147 <tstamp prefix="build">
148 <format property="date" pattern="dd MMMM yyyy"/>
150 <properties file="${outputDir}/.build_properties">
152 ---Jalview Build Details---
154 <property name="VERSION" value="${JALVIEW_VERSION}"/>
155 <property name="BUILD_DATE" value="${build.date}"/>
160 <target name="clean" depends="init">
161 <!-- not efficient yet. -->
162 <delete dir="${outputDir}"/>
165 <target name="distclean" depends="init, clean">
167 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
170 <include name="${outputJar}"/>
171 <include name="#*#"/>
172 <include name="#*.*#"/>
173 <include name="**/#*#"/>
174 <include name="**/#*.*#"/>
176 <include name="*.*~"/>
177 <include name="**/*~"/>
178 <include name="**/*.*~"/>
183 <target name="prepare" depends="init">
184 <mkdir dir="${outputDir}"/>
185 <copy todir="${outputDir}">
187 <include name="${docDir}/**/*.*"/>
188 <include name="${helpDir}/**/*.*"/>
189 <include name="${libDir}/*.jar"/>
191 <fileset dir="${resourceDir}">
192 <include name="**/*.*"/>
197 <target name="build" depends="prepare">
198 <!-- not efficient yet. -->
199 <javac source="1.4" target="1.4"
200 srcdir ="${sourceDir}"
201 destdir="${outputDir}"
202 debug="${javac.debug}"
203 classpathref="build.classpath">
204 <exclude name="jalview/*applet*"/>
205 <exclude name="com/stevesoft/**"/>
208 <target name="buildindices" depends="init, prepare"
209 unless="help.uptodate">
211 classname="com.sun.java.help.search.Indexer"
212 classpathref="build.classpath"
214 dir="${outputDir}/${helpDir}"
220 <target name="makefulldist" depends="makedist">
221 <!-- the default keystore details might need to be edited here -->
223 storepass="${jalview.keystore.pass}"
224 keypass="${jalview.key.pass}"
225 keystore="${jalview.keystore}"
226 alias="${jalview.key}"
231 <fileset dir="${packageDir}">
232 <include name="*.jar"/>
235 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
237 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
238 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
239 <jnlp toFile="${packageDir}/jalview.jnlp"
240 codebase="${WebStartLocation}">
242 <title>Jalview</title>
243 <vendor>The Barton Group</vendor>
244 <homepage href="http://www.jalview.org"/>
245 <description>Jalview Multiple Alignment Editor</description>
246 <description kind="short">Jalview</description>
247 <icon href="logo_big.gif"/>
250 <association mime-type="application-x/ext-file" extensions="fa"/>
251 <association mime-type="application-x/ext-file" extensions="fasta"/>
252 <association mime-type="application-x/ext-file" extensions="fastq"/>
253 <association mime-type="application-x/ext-file" extensions="blc"/>
254 <association mime-type="application-x/ext-file" extensions="msf"/>
255 <association mime-type="application-x/ext-file" extensions="pfam"/>
256 <association mime-type="application-x/ext-file" extensions="aln"/>
257 <association mime-type="application-x/ext-file" extensions="pir"/>
258 <association mime-type="application-x/ext-file" extensions="amsa"/>
262 <j2se version="1.4+"/>
263 <fileset dir="${packageDir}">
264 <include name="jalview.jar"/>
266 <fileset dir="${packageDir}">
267 <include name="*.jar"/>
268 <include name="*_*.jar"/>
269 <exclude name="jalview.jar"/>
271 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
273 <application_desc main_class="jalview.bin.Jalview">
280 <target name="runenv" depends="init">
281 <path id="run.classpath">
282 <pathelement location="${outputDir}"/>
283 <fileset dir="${outputDir}">
284 <include name="${libDir}/*.jar"/>
287 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
289 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
293 <target name="buildextclients" depends="init">
294 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
295 validargs="Y,y,n,N" defaultvalue="N"
296 addproperty="doextbuild.response"/>
297 <condition property="dontextbuild">
298 <equals arg1="n" arg2="${doextbuild.response}"/>
300 <condition property="dontextbuild">
301 <equals arg1="N" arg2="${doextbuild.response}"/>
303 <fail if="dontextbuild">
304 Build External Client Code process aborted by user. Jalview source is unchanged.
306 <!-- Currently, this doesn't happen automatically.
307 1. Run WSDL2Java as below, which generates an ext.vamsas +
308 vamsas.<datapackages> fileset.
309 2. refactor ext.vamsas.SpecificserviceWS* to
310 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
311 3. Update the jalview.ws.*WServices classes to reflect the
312 interface type, and all locations of this wsdl type that Jalview
316 <path id="axisbuild">
317 <path refid="build.classpath"/>
319 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
321 <fileset dir="${sourceDir}" id="client">
322 <include name="${wsdl.ClientNS}/*.*"/>
327 output="${sourceDir}"
331 deployscope="Request"
338 namespace="${wsdl.Namespace}"
339 package="${wsdl.ClientNS}"
341 <mapping namespace="http://dataTypes.vamsas"
342 package="${wsdl.ClientNS}"/>
347 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
348 <!-- make the package jar -->
349 <mkdir dir="${packageDir}"/>
351 <jar destfile="${packageDir}/${outputJar}">
353 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
355 <fileset dir="${outputDir}/">
356 <exclude name="cache*/**"/>
357 <exclude name="*.jar" />
358 <exclude name="*.jar.*" />
359 <exclude name="**/*.jar" />
360 <exclude name="**/*.jar.*" />
364 <copy toDir="${packageDir}" flatten="true">
365 <fileset dir="${outputDir}">
366 <include name="*.jar"/>
367 <include name="**/*.jar"/>
373 <!-- jalopy code reformatter -->
374 <target name="sourcescrub" depends="init,build">
375 <jalopy destdir="jsrc" classpathref="run.classpath"
376 convention="jalview-jalopy.xml">
377 <fileset dir="${sourceDir}">
378 <include name="*.java"/>
379 <include name="**/*.java"/>
380 <include name="**/**/*.java"/>
387 <!-- Compile, package and obfuscate Jalview Applet -->
388 <target name="makeApplet" depends="obfuscate"/>
390 <target name="compileApplet" depends="init,clean">
391 <mkdir dir="${outputDir}"/>
394 srcdir="${sourceDir}"
395 destdir="${outputDir}"
396 debug="${javac.debug}"
397 classpath="lib/${jmolJar}"
398 includes="jalview/appletgui/**"
399 excludes="ext/**,MCview/**,org/**,vamsas/**"
403 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
404 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
405 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
406 <jar destfile="in.jar">
408 <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
410 <fileset dir="${outputDir}">
411 <include name="com/**"/>
412 <include name="MCview/**"/>
413 <include name="jalview/**"/>
414 <include name=".build_properties"/>
415 <include name="images/idwidth.gif"/>
416 <include name="images/link.gif"/>
420 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
422 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
423 <copy file="in.jar" tofile="${jalviewLiteJar}" />
424 <delete file="in.jar"/>
426 <target name="-obfuscatereally" unless="donotobfuscate">
428 <path id="obfuscateDeps.path">
429 <pathelement location="${applet.jre.tools}"/>
430 <pathelement location="lib/${jmolJar}"/>
432 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
435 <injar file="in.jar"/>
436 <outjar file="${jalviewLiteJar}"/>
437 <libraryjar refid="obfuscateDeps.path"/>
438 <keep access="public" type="class"
439 name="jalview.bin.JalviewLite">
440 <field access="public"/>
441 <method access="public"/>
442 <constructor access="public"/>
444 <!-- -libraryjars "${obfuscateDeps}"
446 -outjars jalviewApplet.jar
447 -keep public class jalview.bin.JalviewLite
450 <delete file="in.jar"/>
453 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
454 <taskdef name="castor-srcgen"
455 classname="org.castor.anttask.CastorCodeGenTask"
456 classpathref="build.classpath" />
458 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
459 <include name="*.java"/>
460 <include name="descriptors/*.java"/>
463 <castor-srcgen file="${schemaDir}/vamsas.xsd"
465 package="jalview.schemabinding.version2"
469 properties="${schemaDir}/jalview.properties"
471 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
473 package="jalview.schemabinding.version2"
477 properties="${schemaDir}/jalview.properties"
479 <castor-srcgen file="${schemaDir}/jalview.xsd"
481 package="jalview.schemabinding.version2"
485 properties="${schemaDir}/jalview.properties"
489 now build the jalview.binding package with the old schema set
492 <fileset dir="${sourceDir}/jalview/binding/">
496 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
498 package="jalview.binding"
502 properties="${schemaDir}/jalview.nodesc.properties"
504 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
506 package="jalview.binding"
510 properties="${schemaDir}/jalview.nodesc.properties"
512 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
514 package="jalview.binding"
518 properties="${schemaDir}/jalview.nodesc.properties"
521 <target name="sourcedist" description="create jalview source distribution" depends="init">
522 <delete file="${source.dist.name}"/>
523 <tar destfile="${source.dist.name}" compression="gzip">
524 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
525 <include name="LICENSE"/>
526 <include name="README"/>
527 <include name="build.xml"/>
528 <include name="jalview-jalopy.xml"/>
529 <include name="JalviewApplet.jpx"/>
530 <include name="JalviewX.jpx"/>
531 <include name="${sourceDir}/*.java"/>
532 <include name="${sourceDir}/**/*.java"/>
533 <include name="${sourceDir}/**/*.cdr"/>
534 <include name="${libDir}/**/*"/>
535 <include name="${resourceDir}/**/*"/>
536 <include name="${helpDir}/**/*"/>
537 <exclude name="**/*locales"/>
538 <exclude name="*locales/**"/>
539 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
540 <exclude name="utils/InstallAnywhere/**Build*/**"/>
541 <exclude name="utils/InstallAnywhere/**Build*/**"/>
542 <exclude name="utils/InstallAnywhere/**locale*"/>
543 <exclude name="utils/InstallAnywhere/**locale*/**"/>
544 <include name="${schemaDir}/**/*"/>
545 <include name="utils/**/*"/>
546 <include name="${docDir}/**/*"/>